Escherichia coli K-12 substr. MG1655 Polypeptide: DNA repair; excision nuclease subunit B

Gene: uvrB Accession Numbers: EG11062 (EcoCyc), b0779, ECK0768

Synonyms: dar-1, dar-6

Regulation Summary Diagram: ?

Regulation summary diagram for uvrB

Component of: UvrABC Nucleotide Excision Repair Complex (extended summary available)

UvrB is a subunit of the nucleotide excision repair (NER) complex, UvrA2B, which, along with UvrC, make up the components of the NER generalized DNA repair process which is responsible for repair of an assortment of DNA lesions.

uvrB insertion mutants were identified in a genetic screen for genes that are important for survival of exposure to ionizing radiation (IR). A uvrB deletion mutant has a substantial decrease in IR survival [Byrne14].

Gene Citations: [Sancar82, Schendel82]

Locations: cytosol

Map Position: [812,749 -> 814,770] (17.52 centisomes, 63°)
Length: 2022 bp / 673 aa

Molecular Weight of Polypeptide: 76.226 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0002658 , CGSC:20 , DIP:DIP-48012N , EchoBASE:EB1055 , EcoGene:EG11062 , EcoliWiki:b0779 , Mint:MINT-1244062 , OU-Microarray:b0779 , PortEco:uvrB , PR:PRO_000024199 , Pride:P0A8F8 , Protein Model Portal:P0A8F8 , RefSeq:NP_415300 , RegulonDB:EG11062 , SMR:P0A8F8 , String:511145.b0779 , UniProt:P0A8F8

Relationship Links: InterPro:IN-FAMILY:IPR001650 , InterPro:IN-FAMILY:IPR001943 , InterPro:IN-FAMILY:IPR004807 , InterPro:IN-FAMILY:IPR006935 , InterPro:IN-FAMILY:IPR014001 , InterPro:IN-FAMILY:IPR024759 , InterPro:IN-FAMILY:IPR027417 , Panther:IN-FAMILY:PTHR24029 , PDB:Structure:1E52 , PDB:Structure:1QOJ , Pfam:IN-FAMILY:PF00271 , Pfam:IN-FAMILY:PF02151 , Pfam:IN-FAMILY:PF04851 , Pfam:IN-FAMILY:PF12344 , Prosite:IN-FAMILY:PS50151 , Prosite:IN-FAMILY:PS51192 , Prosite:IN-FAMILY:PS51194 , Smart:IN-FAMILY:SM00487 , Smart:IN-FAMILY:SM00490

In Paralogous Gene Group: 49 (7 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for uvrB

GO Terms:

Biological Process: GO:0006281 - DNA repair Inferred by computational analysis [UniProtGOA11]
GO:0006289 - nucleotide-excision repair Inferred by computational analysis [GOA06, GOA01]
GO:0006974 - cellular response to DNA damage stimulus Inferred by computational analysis [UniProtGOA11]
GO:0009432 - SOS response Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0003677 - DNA binding Inferred by computational analysis [GOA06, GOA01]
GO:0004386 - helicase activity Inferred by computational analysis [GOA06]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
GO:0009381 - excinuclease ABC activity Inferred by computational analysis [GOA06, GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0009380 - excinuclease repair complex Inferred from experiment [Verhoeven02]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes protection radiation
cell processes SOS response
information transfer DNA related DNA degradation
information transfer DNA related DNA repair
metabolism degradation of macromolecules DNA

Essentiality data for uvrB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Subunit of: UvrABC Nucleotide Excision Repair Complex

Synonyms: excinuclease ABC, UvrABC excinuclease, excinuclease UvrABC, excision nuclease ABC, UvrABC system excision endonuclease, ABC excision nuclease

Subunit composition of UvrABC Nucleotide Excision Repair Complex = [UvrB][UvrC][UvrA]
         DNA repair; excision nuclease subunit B = UvrB (summary available)
         excinuclease ABC, subunit C; repair of UV damage to DNA = UvrC (summary available)
         excision nuclease subunit A = UvrA (summary available)

Nucleotide excision repair (NER) is a generalized DNA repair process which can repair a wide diversity of DNA lesion including UV-induced photoproducts (cyclobutane dimers, 6-4 photoproducts, thymine glycol), bulky adducts, apurininc/apyrimidinic (AP) sites and cross-links. While some of these are also repaired by other pathways, in most cases NER is the major pathway for their repair. The nucleotide excision repair pathway consists of the following steps: recognition of the damaged area; incision 3' and 5' to the damaged area; excision of the lesion-containing oligonucleotide; resynthesis of the excised strand and ligation to form a repaired duplex. The main constituents of the pathway are the products of the genes uvrA, uvrB and uvrC [Lin89].

Recognition of the damaged region is carried out in E. coli by UvrA which has been found to exist as a monomer in the absence of ATP but in the presence of ATP it forms homodimers [Sancar88]. The most stable dimer of UvrA contains a mixture of ADP and ATP which is formed upon hydrolysis [Wagner09b] although other studies have shown that UvrA dimerization is stimulated by ATP binding but not hydrolysis [Oh89]. UvrA contains two ATP binding sites and three other structural motifs-- two zinc fingers and a helix-turn-helix motif, which are thought to be required for the proper recognition of damaged DNA substrate [Wang93e]. UvrA binds DNA as a dimer with a strong preference for DNA ends [Wagner09b].

In vitro studies at physiological concentrations show that UvrA associates with UvrB to form a (UvrA2)UvrB complex in an ATP-dependent interaction [Orren89]. The complex has been shown to have a higher binding affinity for damaged DNA than for undamaged DNA [Sancar88]. Purification studies of the complex binding characteristics [Oh86] suggest that the UvrA2B complex tracks along the DNA until a damage site is located. Experimental evidence [Zou99] strongly suggests that UvrA2B complex possesses a helicase activity allowing it to unwind the double stranded DNA permitting access to the adduct by UvrB resulting in dynamic damage recognition and subsequent UvrB binding.

UvrC protein has a high affinity for the UvrB-DNA complex (the UvrA subunits having dissociated concomitant with damage site recognition and attachment). The UvrC protein is the endonucleolytic component of the nucleotide excision complex and it consists of two functional parts with the N-terminal half containing the 3' incision catalytic domain incising first after which the C-terminal half containing the 5' incision catalytic domain performs the second incision [Sancar88]. The UvrD helicase (helicase II) has been implicated in removal of the lesion-containing oligonucleotide and disassembly of the repair complex [Orren92]. An additional endonuclease (the ydjQ gene product-or Cho for UvrC Homologue) has been shown to share significant sequence homology with the N-terminal half of UvrC [Moolenaar02] and is capable of even more efficient 3' incision than UvrC.

In E. coli, NER occurs at a higher rate on the transcribed strand of actively transcribed genes (compared to the non-transcribed strand of the same gene or non-transcribed regions of the genome). This transcription-coupled repair (TCR) activity has been ascribed to a protein called the 'transcription-repair coupling factor' which in E.coli is the product of the mfd (mutation frequency decline) gene [Selby93]. A second pathway for TCR, involving the DNA helicase protein UvrD has also been characterised in E. coli K-12. In this pathway UvrD, in conjuction with NusA, clears lesions by forcing obstructed elongation complexes to backtrack, allowing UvrABC to gain access to damaged sites [Epshtein14]. UvrD mediated TCR facilitates NER without the loss of RNA polymerase which enables prompt resumption of transcription [Epshtein14].

UvrA is one of a series of genes known as SOS genes which, in the event of DNA damage and other stresses, are induced to increased transcription levels. UvrA is constitutively expressed in E. coli at a level of ~ 25 molecules per cell but SOS-mediated induction of its gene increases the level to ~ 250 molecules per cell. UvrB and UvrD are also inducible by DNA damage. UvrC is not induced in the SOS response, however its homolog, Cho, is.

Reviews: [Van94, Spivak14]
Comment: [Artsimovitch14]

Citations: [Bugay14]

Enzymatic reaction of: Nucleotide excision repair (UvrABC Nucleotide Excision Repair Complex)

Synonyms: excinuclease, excision endonuclease, excision nuclease

EC Number: 3.1.25.-

DNA with lesion + H2O <=> DNA without lesion

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Sequence Features

Protein sequence of DNA repair; excision nuclease subunit B with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Arikan86, UniProt11a]
UniProt: Removed.
Chain 2 -> 673
UniProt: UvrABC system protein B;
Conserved-Region 26 -> 415
UniProt: Helicase ATP-binding;
Nucleotide-Phosphate-Binding-Region 39 -> 46
UniProt: ATP; Non-Experimental Qualifier: potential;
Protein-Segment 92 -> 115
UniProt: Beta-hairpin; Sequence Annotation Type: short sequence motif.
Mutagenesis-Variant 95 -> 96
[Moolenaar01, UniProt15]
UniProt: Defective in DNA-unwinding activity.
Mutagenesis-Variant 101
[Moolenaar01, UniProt11a]
UniProt: Defective in DNA-unwinding activity; when associated with A-108.
Mutagenesis-Variant 108
[Moolenaar01, UniProt11a]
UniProt: Defective in DNA-unwinding activity; when associated with A-101.
Conserved-Region 431 -> 597
UniProt: Helicase C-terminal;
Sequence-Conflict 477
[Arikan86, UniProt10a]
UniProt: (in Ref. 1; CAA27314);
Amino-Acid-Site 630, 631
UniProt: Cleavage; Sequence Annotation Type: site; Non-Experimental Qualifier: potential;
Conserved-Region 633 -> 668
UniProt: UVR;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b0779 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11062; confirmed by SwissProt match.


Arikan86: Arikan E, Kulkarni MS, Thomas DC, Sancar A (1986). "Sequences of the E. coli uvrB gene and protein." Nucleic Acids Res 14(6);2637-50. PMID: 3515321

Artsimovitch14: Artsimovitch I (2014). "Molecular biology: The tug of DNA repair." Nature 505(7483);298-9. PMID: 24402229

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bugay14: Bugay AN, Krasavin EA, Parkhomenko AY, Vasilyeva MA (2014). "Modeling nucleotide excision repair and its impact on UV-induced mutagenesis during SOS-response in bacterial cells." J Theor Biol 364C;7-20. PMID: 25195002

Byrne14: Byrne RT, Chen SH, Wood EA, Cabot EL, Cox MM (2014). "Escherichia coli genes and pathways involved in surviving extreme exposure to ionizing radiation." J Bacteriol 196(20);3534-45. PMID: 25049088

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Epshtein14: Epshtein V, Kamarthapu V, McGary K, Svetlov V, Ueberheide B, Proshkin S, Mironov A, Nudler E (2014). "UvrD facilitates DNA repair by pulling RNA polymerase backwards." Nature 505(7483);372-7. PMID: 24402227

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Lin89: Lin JJ, Sancar A (1989). "A new mechanism for repairing oxidative damage to DNA: (A)BC excinuclease removes AP sites and thymine glycols from DNA." Biochemistry 28(20);7979-84. PMID: 2690930

Moolenaar01: Moolenaar GF, Hoglund L, Goosen N (2001). "Clue to damage recognition by UvrB: residues in the beta-hairpin structure prevent binding to non-damaged DNA." EMBO J 20(21);6140-9. PMID: 11689453

Moolenaar02: Moolenaar GF, van Rossum-Fikkert S, van Kesteren M, Goosen N (2002). "Cho, a second endonuclease involved in Escherichia coli nucleotide excision repair." Proc Natl Acad Sci U S A 99(3);1467-72. PMID: 11818552

Oh86: Oh EY, Grossman L (1986). "The effect of Escherichia coli Uvr protein binding on the topology of supercoiled DNA." Nucleic Acids Res 14(21);8557-71. PMID: 3024109

Oh89: Oh EY, Claassen L, Thiagalingam S, Mazur S, Grossman L (1989). "ATPase activity of the UvrA and UvrAB protein complexes of the Escherichia coli UvrABC endonuclease." Nucleic Acids Res 17(11);4145-59. PMID: 2525700

Orren89: Orren DK, Sancar A (1989). "The (A)BC excinuclease of Escherichia coli has only the UvrB and UvrC subunits in the incision complex." Proc Natl Acad Sci U S A 86(14);5237-41. PMID: 2546148

Orren92: Orren DK, Selby CP, Hearst JE, Sancar A (1992). "Post-incision steps of nucleotide excision repair in Escherichia coli. Disassembly of the UvrBC-DNA complex by helicase II and DNA polymerase I." J Biol Chem 267(2);780-8. PMID: 1530937

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Sancar82: Sancar GB, Sancar A, Little JW, Rupp WD (1982). "The uvrB gene of Escherichia coli has both lexA-repressed and lexA-independent promoters." Cell 1982;28(3);523-30. PMID: 6280873

Sancar88: Sancar A, Sancar GB (1988). "DNA repair enzymes." Annu Rev Biochem 57;29-67. PMID: 3052275

Schendel82: Schendel PF, Fogliano M, Strausbaugh LD (1982). "Regulation of the Escherichia coli K-12 uvrB operon." J Bacteriol 1982;150(2);676-85. PMID: 6802798

Selby93: Selby CP, Sancar A (1993). "Transcription-repair coupling and mutation frequency decline." J Bacteriol 175(23);7509-14. PMID: 8244919

Spivak14: Spivak G, Ganesan AK (2014). "The complex choreography of transcription-coupled repair." DNA Repair (Amst). PMID: 24751236

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Van94: Van Houten B, McCullough A (1994). "Nucleotide excision repair in E. coli." Ann N Y Acad Sci 726;236-51. PMID: 8092680

Verhoeven02: Verhoeven EE, Wyman C, Moolenaar GF, Goosen N (2002). "The presence of two UvrB subunits in the UvrAB complex ensures damage detection in both DNA strands." EMBO J 21(15);4196-205. PMID: 12145219

Wagner09b: Wagner K, Moolenaar G, van Noort J, Goosen N (2009). "Single-molecule analysis reveals two separate DNA-binding domains in the Escherichia coli UvrA dimer." Nucleic Acids Res 37(6);1962-72. PMID: 19208636

Wang93e: Wang J, Grossman L (1993). "Mutations in the helix-turn-helix motif of the Escherichia coli UvrA protein eliminate its specificity for UV-damaged DNA." J Biol Chem 268(7);5323-31. PMID: 8444906

Zou99: Zou Y, Van Houten B (1999). "Strand opening by the UvrA(2)B complex allows dynamic recognition of DNA damage." EMBO J 18(17);4889-901. PMID: 10469667

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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